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Crystal Structure of P450 OxyD that is involved in the Biosynthesis of Vancomycin-type Antibiotics
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EJB PDB ENTRY 3EJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 18% PEG 2000 MME, 0.1M Bis-Tris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.85 α = 90 b = 61.05 β = 102.48 c = 100.64 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2009-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99986 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 20 97.5 0.06 19.2 7.9 45824 44661 3 32.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.2 92.4 0.3 4.5 8 5487
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3EJB 2.1 19.75 45824 43424 2286 100 0.20913 0.20786 0.2283 0.23302 0.2508 RANDOM 22.757
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.42 -0.71 0.79 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_3_deg 13.376 r_dihedral_angle_4_deg 10.39 r_dihedral_angle_1_deg 4.162 r_angle_refined_deg 0.884 r_scangle_it 0.691 r_scbond_it 0.408 r_mcangle_it 0.287 r_mcbond_it 0.152 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_3_deg 13.376 r_dihedral_angle_4_deg 10.39 r_dihedral_angle_1_deg 4.162 r_angle_refined_deg 0.884 r_scangle_it 0.691 r_scbond_it 0.408 r_mcangle_it 0.287 r_mcbond_it 0.152 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5968 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 146
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling